Suggested settings for CCS reads

[davidlougheed]

PacBio CCS reads have a very different error profile to standard PacBio CLRs. Are there suggested HMM settings for genotyping CCS reads, in a context where I do not have access to subreads (even though as suggested in the 2017 paper they'd be better-performing)?

[liuqianhn]

@davidlougheed I do not have specific parameter for PacBio CCS reads. But I assume that CCS reads have similar error profile as illumina reads, and you can try to use --SplitAndReAlign 2 --SeqTech "Illumina" to see whether you have different results.